Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9

Nurul Azmina Binti Abdul Malik, Kalaivani K. Nadarajah

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Chitin is a microbe-associated molecular pattern (MAMP) molecule in fungal cell wall that functions as elicitor which induces immune response in plants. Plants have its own defence system to protect itself from any invasion of pathogens. Chitin Elicitor Binding Protein (CEBiP) is one of the plant pattern recognition receptors (PRRs) that will detect the presence of the pathogen-associated molecular patterns (PAMPs) and activate plant defence system. In this study, we used Oryza sativa variety UKMRC9 to study the function of Chitin Elicitor Binding Protein (CEBiP) gene in plant immune system. The sample was extracted and amplified using the primer that were specifically designed for CEBiP based on the full gene sequence obtained from MSU Rice Genome Annotation Project database. The sample then was transformed into pGEM-T cloning vector. The plasmid construct of vector pCAMBIA 1305.2 was completed using PmII and BstEII as the restriction enzyme. The sequencing results of pGEM-T-CEBiP-RC9 obtained are subjected to multiple sequence alignment and the generation of a phylogenetic tree. Analysis obtained from BLAST shows that CEBiP UKMRC9 has 100% identity with four sequences from NCBI database with high query coverage. Multiple sequence alignment also shows that there are some nucleotides that have been inserted and deleted (indels) in the amplified sequence. Pairwise alignment indicates high similarity between CEBiP UKMRC9 and Chitin elicitor binding protein [Oryza sativa Japonica Group], PREDICTED: chitin elicitor-binding protein [Oryza sativa Japonica Group], Chain A, Crystal Structure of Oscebip, Chain A, and Crystal Structure of Oscebip Complex in BLAST. Results from phylogeny analysis places CEBiP UKMRC9 under the same clade with Oryza sativa cv Nipponbare CEBiP MSU. Even within the graminaceae, there is cladal separation of organisms based on genus and species.

Original languageEnglish
Title of host publication2018 UKM FST Postgraduate Colloquium
Subtitle of host publicationProceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium
EditorsNoor Hayati Ahmad Rasol, Kamarulzaman Ibrahim, Siti Aishah Hasbullah, Mohammad Hafizuddin Hj. Jumali, Nazlina Ibrahim, Marlia Mohd Hanafiah, Mohd Talib Latif
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735418431
DOIs
Publication statusPublished - 27 Jun 2019
Event2018 UKM FST Postgraduate Colloquium - Selangor, Malaysia
Duration: 4 Apr 20186 Apr 2018

Publication series

NameAIP Conference Proceedings
Volume2111
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

Conference2018 UKM FST Postgraduate Colloquium
CountryMalaysia
CitySelangor
Period4/4/186/4/18

Fingerprint

chitin
genes
binding proteins
isolation
Oryza sativa
proteins
protein
gene
pathogens
alignment
sequence alignment
crystal structure
elicitors
pathogen
annotations
genetic vectors
immune systems
plasmid vectors
primers
plant defense

Keywords

  • Chitin Elicitor Binding Protein
  • Oryza sativa
  • Pathogen/Microbe-associated Molecular Pattern (PAMPs/MAMPs)
  • pCAMBIA 1305.2

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Plant Science
  • Physics and Astronomy(all)
  • Nature and Landscape Conservation

Cite this

Malik, N. A. B. A., & K. Nadarajah, K. (2019). Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9. In N. H. A. Rasol, K. Ibrahim, S. A. Hasbullah, M. H. H. Jumali, N. Ibrahim, M. M. Hanafiah, & M. T. Latif (Eds.), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium [060019] (AIP Conference Proceedings; Vol. 2111). American Institute of Physics Inc.. https://doi.org/10.1063/1.5111281

Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9. / Malik, Nurul Azmina Binti Abdul; K. Nadarajah, Kalaivani.

2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. ed. / Noor Hayati Ahmad Rasol; Kamarulzaman Ibrahim; Siti Aishah Hasbullah; Mohammad Hafizuddin Hj. Jumali; Nazlina Ibrahim; Marlia Mohd Hanafiah; Mohd Talib Latif. American Institute of Physics Inc., 2019. 060019 (AIP Conference Proceedings; Vol. 2111).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Malik, NABA & K. Nadarajah, K 2019, Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9. in NHA Rasol, K Ibrahim, SA Hasbullah, MHH Jumali, N Ibrahim, MM Hanafiah & MT Latif (eds), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium., 060019, AIP Conference Proceedings, vol. 2111, American Institute of Physics Inc., 2018 UKM FST Postgraduate Colloquium, Selangor, Malaysia, 4/4/18. https://doi.org/10.1063/1.5111281
Malik NABA, K. Nadarajah K. Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9. In Rasol NHA, Ibrahim K, Hasbullah SA, Jumali MHH, Ibrahim N, Hanafiah MM, Latif MT, editors, 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. American Institute of Physics Inc. 2019. 060019. (AIP Conference Proceedings). https://doi.org/10.1063/1.5111281
Malik, Nurul Azmina Binti Abdul ; K. Nadarajah, Kalaivani. / Isolation and characterisation of chitin elicitor binding protein (CEBiP) gene in Oryza sativa variety UKMRC9. 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. editor / Noor Hayati Ahmad Rasol ; Kamarulzaman Ibrahim ; Siti Aishah Hasbullah ; Mohammad Hafizuddin Hj. Jumali ; Nazlina Ibrahim ; Marlia Mohd Hanafiah ; Mohd Talib Latif. American Institute of Physics Inc., 2019. (AIP Conference Proceedings).
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abstract = "Chitin is a microbe-associated molecular pattern (MAMP) molecule in fungal cell wall that functions as elicitor which induces immune response in plants. Plants have its own defence system to protect itself from any invasion of pathogens. Chitin Elicitor Binding Protein (CEBiP) is one of the plant pattern recognition receptors (PRRs) that will detect the presence of the pathogen-associated molecular patterns (PAMPs) and activate plant defence system. In this study, we used Oryza sativa variety UKMRC9 to study the function of Chitin Elicitor Binding Protein (CEBiP) gene in plant immune system. The sample was extracted and amplified using the primer that were specifically designed for CEBiP based on the full gene sequence obtained from MSU Rice Genome Annotation Project database. The sample then was transformed into pGEM-T cloning vector. The plasmid construct of vector pCAMBIA 1305.2 was completed using PmII and BstEII as the restriction enzyme. The sequencing results of pGEM-T-CEBiP-RC9 obtained are subjected to multiple sequence alignment and the generation of a phylogenetic tree. Analysis obtained from BLAST shows that CEBiP UKMRC9 has 100{\%} identity with four sequences from NCBI database with high query coverage. Multiple sequence alignment also shows that there are some nucleotides that have been inserted and deleted (indels) in the amplified sequence. Pairwise alignment indicates high similarity between CEBiP UKMRC9 and Chitin elicitor binding protein [Oryza sativa Japonica Group], PREDICTED: chitin elicitor-binding protein [Oryza sativa Japonica Group], Chain A, Crystal Structure of Oscebip, Chain A, and Crystal Structure of Oscebip Complex in BLAST. Results from phylogeny analysis places CEBiP UKMRC9 under the same clade with Oryza sativa cv Nipponbare CEBiP MSU. Even within the graminaceae, there is cladal separation of organisms based on genus and species.",
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